BioC 3.4: CHECK report for oligoClasses on malbec1

Package: oligoClasses

Version: 1.36.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.36.0.tar.gz

StartedAt: 2017-04-15 00:12:33 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:15:47 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 193.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/oligoClasses.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘doRedis’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oligoClasses’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getSequenceLengths: no visible binding for global variable ‘seqlengths’
pdPkgFromBioC: no visible binding for global variable ‘contrib.url’
pdPkgFromBioC: no visible global function definition for
  ‘available.packages’
pdPkgFromBioC: no visible global function definition for
  ‘install.packages’
chromosome,gSetList: no visible global function definition for
  ‘chromosomeList’
coerce,CNSet-CopyNumberSet: no visible global function definition for
  ‘totalCopynumber’
geometry,FeatureSet: no visible global function definition for ‘getPD’
Undefined global functions or variables:
  available.packages chromosomeList contrib.url getPD install.packages
  seqlengths totalCopynumber
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "install.packages")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNSet,ANY,ANY,ANY'
  generic '[' and siglist 'gSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
GenomeAnnotatedDataFrame-class 0.88   0.12   5.696
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.

* installing *source* package ‘oligoClasses’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.360	0.000	0.361
AssayData-methods	0.852	0.024	0.888
AssayDataList	0.004	0.000	0.001
BeadStudioSet-class	0.352	0.000	0.351
CNSet-class	0.036	0.000	0.037
CopyNumberSet-class	0.028	0.000	0.028
CopyNumberSet-methods	0.124	0.028	0.155
FeatureSetExtensions-class	0.108	0.000	0.110
GRanges-methods	0.252	0.020	0.270
GenomeAnnotatedDataFrame-class	0.880	0.120	5.696
GenomeAnnotatedDataFrameFrom-methods	1.276	0.020	1.377
SnpSet-methods	0.040	0.000	0.038
SnpSet2-class	0.028	0.000	0.028
SnpSuperSet-class	0.060	0.000	0.057
affyPlatforms	0.000	0.000	0.001
batch	0.032	0.000	0.033
celfileDate	0.024	0.004	0.078
celfileName	0.000	0.000	0.001
checkExists	0.008	0.000	0.009
checkOrder	0.312	0.004	0.328
chromosome-methods	0.004	0.000	0.001
chromosome2integer	0.000	0.000	0.001
clusterOpts	0.000	0.000	0.001
data-efsExample	0.000	0.000	0.002
data-scqsExample	0.000	0.000	0.002
data-sfsExample	0.004	0.000	0.001
data-sqsExample	0.000	0.000	0.003
db	0	0	0
ff_matrix	0.000	0.000	0.001
ff_or_matrix-class	0.004	0.000	0.001
fileConnections	0.000	0.000	0.001
flags	0.040	0.008	0.047
gSet-class	0.000	0.000	0.001
gSetList-class	0.004	0.000	0.001
genomeBuild	0.004	0.000	0.003
geometry-methods	0.632	0.000	0.633
getBar	0.004	0.000	0.000
getSequenceLengths	0.096	0.000	0.099
i2p_p2i	0.000	0.000	0.001
integerMatrix	0.004	0.000	0.000
is.ffmatrix	0.000	0.000	0.001
isPackageLoaded	0.000	0.000	0.001
kind	0.152	0.004	0.158
largeObjects	0.000	0.000	0.003
ldOpts	0.000	0.000	0.001
library2	0.032	0.000	0.030
list.celfiles	0.012	0.004	0.095
locusLevelData	0.088	0.004	0.094
makeFeatureGRanges	0.376	0.008	0.383
oligoSetExample	0.176	0.004	0.179
pdPkgFromBioC	0.004	0.000	0.001
requireAnnotation	0.000	0.000	0.001
splitVec	0.004	0.000	0.003